Sarah B. Carey, Philip C. Bentz, John T. Lovell, Laramie Aközbek, Zachary A. Myers, Walid Korani, Joshua S. Havill, Lillian Padgitt-Cobb, Ryan C. Lynch, Nicholas Allsing, Jack Mangels, Zachary Stansell, George M. Stack, Tyler Gordon, Austin Osmanski, Katherine A. Easterling, Leonardo R. Orozco, Zach E Marcus, Haley Hale, Hannah McCoy, Zachary Meharg, Jane Grimwood, Lawrence B. Smart, Daniela Vergara, Rafael F. Guerrero, Nolan C. Kane, Rich Fletcher, John K. McKay, Todd P. Michael, Gary J. Muehlbauer, Josh Clevenger, Alex Harkess
Sex chromosomes in cannabis and hop were identified a century ago because of their obvious visible differences in size (heteromorphy). However, we know little about the genes they contain that control the development of the inflorescences. Here we assembled genomes, with phased sex chromosomes, for hop and cannabis. The XY chromosomes share an origin prior to the divergence between the genera around 36 MYA. Due to the inheritance patterns of the XYs, the male-specific region of the Y is highly-degenerated, with substantial gene loss, while the X shows faster rates of molecular evolution. Consistent with the hypothesis that these species lack an active-Y system, no clear sex-determining genes reside on the Y. Instead, an X-linked homolog of aminocyclopropane-1-carboxylate synthase (ACS), that is involved in the ethylene biosynthesis pathway, determines the fate of the female inflorescence. Beyond sex determination, the sex chromosomes contribute to the sexual dimorphism in ecology and physiology and have played a role in the domestication and breeding of these species. The ancient X and Y chromosomes of cannabis and hop display interesting patterns of molecular evolution and harbor key floral genes. Here the authors show that the X chromosome, not the Y, determines sex, and identify an X-linked ethylene biosynthesis gene as a candidate for sex-determination.